Baltimore Scheme- Viral Classification System

Summary

This video from the Brain Boost channel delves into the Baltimore scheme of viral genome classification, covering seven distinct groups. It explains how each group, from double-stranded DNA to plus single-stranded RNA with a DNA intermediate, utilizes host machinery or encodes its own polymerases to produce mRNA and replicate their genomes. The explanation highlights the strategies viruses employ to infect new hosts, emphasizing the importance of mRNA in viral protein synthesis and genome replication.

Takeaways

• 🌟 The Baltimore scheme classifies viral genomes into seven groups based on their genetic material and replication strategies.
• 🧬 Group 1: Double-stranded DNA viruses can use the host's DNA-dependent RNA polymerase to produce mRNA for viral protein synthesis.
• 🌀 Group 2: Single-stranded DNA viruses require a DNA synthesis step to form double-stranded DNA before mRNA production.
• 📚 Group 3: Double-stranded RNA viruses transcribe one of their RNA strands into a positive strand that serves as mRNA and also as a template for the negative strand.
• 📖 Group 4: Positive single-stranded RNA viruses are very infectious as their genome can be directly translated into proteins by the host's ribosomes, exemplified by Coronaviridae.
• ⏪ Group 5: Negative single-stranded RNA viruses must first be copied to a positive strand to serve as mRNA, using their virally encoded RNA-dependent RNA polymerase (RdRP).
• 🔄 Group 6: Positive single-stranded RNA viruses with a double-stranded DNA intermediate use reverse transcriptase to form DNA from their RNA genome, which then integrates into the host genome.
• 🔄 Group 7: Gapped double-stranded DNA viruses need to fill the gap in their DNA before they can proceed with mRNA production and genome replication.
• 🛠️ All viruses aim to express their genes as functional mRNA to direct the host's translational machinery to synthesize viral proteins and replicate their genomes for new infections.
• 🔑 The host's translational machinery can only translate mRNA, which is why all viral groups in the Baltimore scheme eventually produce mRNA as an intermediate step.
• 🔍 The purpose of viral replication strategies is to efficiently produce mRNA for protein synthesis and duplicate the viral genome for packaging into new virions to infect additional hosts.

Q & A

What is the Baltimore scheme of viral genome classification?

The Baltimore scheme is a system for classifying viruses based on the type of nucleic acid they contain and their method of replication. It is named after David Baltimore and categorizes viruses into seven groups.

What are the seven groups in the Baltimore scheme?

The seven groups are: 1) Double-stranded DNA, 2) Single-stranded DNA, 3) Double-stranded RNA, 4) Positive single-stranded RNA, 5) Negative single-stranded RNA, 6) Positive single-stranded RNA with a double-stranded DNA intermediate, and 7) Gapped double-stranded DNA.

Why is mRNA important in the context of viral replication?

MRNA is important because it is the form of genetic material that can be directly translated by the host's ribosomes to produce viral proteins, which is a necessary step for viral replication and infection.

What is the role of the host's translational machinery in viral replication?

The host's translational machinery is used by viruses to translate mRNA into viral proteins, which is essential for the production of new viral particles.

How do DNA viruses with limited coding capacity produce mRNA?

DNA viruses with limited coding capacity rely on the host's DNA-dependent RNA polymerase to transcribe their DNA into mRNA.

What is the difference between positive and negative strands in the context of RNA and DNA?

In RNA and DNA, the positive strand is the one that can be directly translated into proteins or used as a template for replication. The negative strand is the complement of the positive strand and must be converted into a positive strand to serve these functions.

Why do RNA viruses need to encode their own polymerases?

RNA viruses need to encode their own polymerases because cells do not have RNA-dependent RNA polymerases, which are necessary for replicating the viral RNA genome or producing mRNA from an RNA template.

What is the purpose of reverse transcriptase in the replication of certain RNA viruses?

Reverse transcriptase, also known as RNA-dependent DNA polymerase, is used by certain RNA viruses to convert their RNA genome into a DNA intermediate, which can then be integrated into the host genome or used for further replication.

How does the process of replication differ between positive and negative single-stranded RNA viruses?

Positive single-stranded RNA viruses can be directly translated into proteins and use their genome as a template for replication. Negative single-stranded RNA viruses must first be transcribed into a positive strand to serve as mRNA and then use this positive strand as a template for replication.

What is the significance of the term 'gapped double-stranded DNA' in the context of viral genomes?

Gapped double-stranded DNA refers to a viral genome that has a break or gap in one of the DNA strands. This gap must be filled before the DNA can be used as a template for replication or transcription into mRNA.

Can you provide an example of a virus that belongs to Group 4 of the Baltimore scheme?

An example of a virus in Group 4 is the coronavirus, which has a positive single-stranded RNA genome that can be directly translated into proteins by the host's ribosomes.

Outlines

00:00

🌟 Introduction to the Baltimore Scheme

This paragraph introduces the Baltimore scheme for viral genome classification, which categorizes viruses into seven groups based on their genome types. The speaker provides an overview of the groups, which include double-stranded DNA, single-stranded DNA, double-stranded RNA, plus single-stranded RNA, negative single-stranded RNA, plus single-stranded RNA with a double-stranded DNA intermediate, and gapped double-stranded DNA. The importance of mRNA in the translation process is emphasized, as all viral genomes must be expressed as functional mRNA to direct the host's translational machinery to synthesize viral proteins. The ultimate goal of viruses is to replicate their genomes and package them into virions for infection of new hosts.

05:00

🧬 DNA Viral Genomes: Groups One, Two, and Seven

This section delves into the specifics of DNA viral genomes, which include groups one (double-stranded DNA), two (single-stranded DNA), and seven (gapped double-stranded DNA). The speaker explains that double-stranded DNA viruses can use the host's DNA-dependent RNA polymerase to produce mRNA. Single-stranded DNA viruses must first convert to double-stranded DNA before mRNA production, while gapped double-stranded DNA viruses need to fill in the gap to form a complete DNA molecule. The process of genome replication and the role of reverse transcriptase in converting RNA back to DNA are also discussed, with examples provided to illustrate these mechanisms.

10:01

📚 RNA Viral Genomes: Groups Three, Four, Five, and Six

The speaker transitions to RNA viral genomes, highlighting the differences between DNA and RNA viruses. RNA viruses cannot rely on the host's polymerase due to the lack of RNA-dependent RNA polymerase in cells. Instead, they must encode their own polymerases. The discussion covers group three (double-stranded RNA), where one strand is transcribed to produce mRNA and the other to duplicate the genome. Group four (positive single-stranded RNA) is particularly infectious as it can be directly translated into proteins. Group five (negative single-stranded RNA) requires the production of a positive strand to serve as mRNA. Finally, group six involves reverse transcriptase to convert the RNA genome into a double-stranded DNA intermediate, which then integrates into the host genome for mRNA production.

15:04

🔬 Conclusion of the Baltimore Scheme Overview

In conclusion, the speaker summarizes the Baltimore scheme, emphasizing the diversity of strategies employed by viruses to replicate their genomes and produce mRNA. The importance of understanding these mechanisms for virology studies is highlighted, and the speaker encourages viewers to subscribe, like, and comment with questions or topic suggestions for future videos. This paragraph wraps up the educational content, providing a comprehensive review of the Baltimore classification system and its relevance to the study of viral genomes.

Keywords

💡Baltimore Scheme

The Baltimore Scheme is a classification system for viral genomes based on the type of nucleic acid they contain and their replication strategy. It is central to the video's theme as it provides the framework for discussing the different groups of viruses. The script delves into each group, explaining their unique characteristics and replication processes.

💡Double-Stranded DNA

Double-Stranded DNA refers to a type of genetic material composed of two complementary strands of nucleotides. In the context of the video, Group 1 viruses have this as their genome. The script explains that these viruses can use the host's DNA-dependent RNA polymerase to produce mRNA for protein synthesis, illustrating the interplay between viral and host mechanisms.

💡Single-Stranded DNA

Single-Stranded DNA is genetic material made up of a single strand of nucleotides. Group 2 viruses possess this type of genome, and the script mentions that they must convert to double-stranded DNA before mRNA production, highlighting the necessity for certain viruses to undergo structural changes to utilize host machinery.

💡Double-Stranded RNA

Double-Stranded RNA consists of two complementary RNA strands. Group 3 viruses are characterized by this genome type. The video script describes how one strand is transcribed into mRNA while the other can serve as a template for replicating the genome, emphasizing the dual role of viral RNA.

💡Positive Single-Stranded RNA

Positive Single-Stranded RNA, also known as mRNA, is a genome type that can be directly translated into proteins by the host's ribosomes. Group 4 viruses, such as coronaviruses mentioned in the script, are infectious due to their ability to immediately utilize host machinery for protein synthesis, underscoring their potential threat to hosts.

💡Negative Single-Stranded RNA

Negative Single-Stranded RNA is a genome type that requires transcription into a positive strand to serve as mRNA. Group 5 viruses initiate their replication by using their encoded RNA-dependent RNA polymerase (RdRP) to create the positive strand, as detailed in the script, which then acts as mRNA or a template for genome replication.

💡Plus Single-Stranded RNA with Double-Stranded DNA Intermediate

This term refers to Group 6 viruses that use reverse transcriptase to convert their RNA genome into a double-stranded DNA intermediate, which then integrates into the host genome. The script explains this process as a means for these viruses to produce mRNA and replicate their genome, highlighting the complexity of their life cycle.

💡Gapped Double-Stranded DNA

Gapped Double-Stranded DNA describes a genome with breaks or gaps in one of the strands. Group 7 viruses, as mentioned in the script, must fill these gaps to form a complete double-stranded DNA molecule, which is then used for mRNA production and genome replication, illustrating the need for repair before replication.

💡RNA Polymerase

RNA Polymerase is an enzyme that synthesizes RNA from a DNA or RNA template. The script discusses how different types of polymerases, such as DNA-dependent RNA polymerase and RNA-dependent RNA polymerase (RdRP), are used by viruses depending on their genome type, emphasizing the enzyme's role in viral replication and mRNA production.

💡Reverse Transcriptase

Reverse Transcriptase is an enzyme that synthesizes DNA from an RNA template. The script explains its role in the replication strategy of Group 6 viruses, where it converts the viral RNA genome into a double-stranded DNA intermediate, demonstrating a unique aspect of some viral life cycles.

💡Encapsidation

Encapsidation is the process by which viral genomes are packaged into viral particles or virions. The script mentions this term in the context of sending replicated genomes for encapsidation, indicating a critical step in the viral life cycle that allows for the spread to new hosts.

Highlights

Introduction to the Baltimore scheme of viral genome classification.

Overview of seven groups of viral genomes and their unique characteristics.

Explanation of the importance of mRNA in the host's translational machinery.

Clarification of the terms 'positive strand' and 'negative strand' in the context of RNA and DNA.

The purpose of viruses to make copies of their genome and package them into virions.

Different strategies used by DNA and RNA viruses to produce mRNA and replicate their genomes.

Group 1: Double-stranded DNA viruses and their reliance on the host's polymerase.

Group 2: Single-stranded DNA viruses and the process of converting to double-stranded DNA for mRNA production.

Group 7: Gapped double-stranded DNA viruses and the necessity to fill gaps before mRNA generation.

The role of reverse transcriptase in RNA to DNA conversion for certain viral genomes.

Group 3: Double-stranded RNA viruses and their method of mRNA production and genome replication.

Group 4: Positive single-stranded RNA viruses and their direct translation into proteins by the host.

Group 5: Negative single-stranded RNA viruses and the need for initial copying to produce mRNA.

Group 6: Positive single-stranded RNA viruses with a double-stranded DNA intermediate.

The use of reverse transcriptase in Group 6 to convert RNA genomes back to DNA.

Summary of the Baltimore scheme and its significance in understanding viral genome strategies.

Transcripts

hello everyone and welcome to the brain

boost

channel so today we're going to be

looking at the baltimore scheme

of viral genome classification so let's

just

jump right into the video

okay so this is just an overview of what

we're going to be looking at today

so here we have seven groups that we're

going to start

tackling individually in a bit i just

want to give a quick

overview and a brief explanation of each

one

and a few points that we should have an

understanding of before we get into the

depth

so here we have group one which is

double-stranded dna

group 2 which is single-stranded dna

we have group 3 which is double-stranded

rna

group 4 which is plus single-stranded

rna

and if you notice something that

that's basically just mrna

we have group 5 which is negative single

stranded rna

we have group 6 which is plus single

stranded rna

with a double-stranded dna intermediate

and we have group seven which is gapped

double-stranded dna

so basically something that we should

keep in mind is that

the host's translational machinery is

it can only translate mrna right

so m this is why

all of these groups in this schematic

this is why they all point

down towards this boxed mrna because

they all have to get here

so mrna is technically defined as

the positive strand because that's what

is

translated by ribosomes and to make

a positive stranded rna from dna

that has to be negative so when we're

looking at rna or dna

the complement of the plus strand is

called the negative strand

and vice versa so

that means that plus strand plus

single stranded rna is

technically just mrna they're the same

thing which is what i mentioned

about group four here and so

uh basically before we get into all the

details about everything

the purpose of the virus is to

basically make copies of its genome

and package these genomes into virions

so that

they can go on and infect new hosts

so this means that all viruses have to

make or express their genes as a

functional mrna

right so that they can direct

you know host translational machinery to

synthesize

viral proteins which is the end product

here at the bottom

we want to get to mrna to make viral

proteins and we want to

duplicate our genome so that we can get

that packaged

and sent off to start infecting new

hosts

so let's just start with

the dna viral genomes so that's groups

one two and seven

um and before we get into the dna

genomes i just want you guys to remember

that when we're looking at viral dna

genomes

all dna viruses have to go to

double-stranded dna so group one

is already double-stranded dna so that

can be

left as is before we get to the mrna

group two is single stranded dna so it

has to become

double stranded first before we can

start working with it and messing around

and the same goes for group seven it's

gapped double-stranded dna so

we have to fill that gap in first before

we have a functional

double-stranded dna that we can mess

around with to get to mrna

so we're going to start with group one

which is our double stranded

dna genome and we're only really going

to focus on

figure a all the other figures here are

just

images of other examples that have this

genome type but we're only looking at

figure a

for the most part so in this case

of double-stranded dna there is a

limited coding capacity here so

you know some smaller genomes they don't

necessarily have space to encode

a polymerase so they're going to depend

or the virus is depending on

the hosts polymerase to produce

the mrna and to do all the work for it

so

in this case when we're starting with

double stranded dna and we're going to

produce an mrna

we're relying on the host's dna

dependent rna polymerase

this is kind of a little bit of a trick

you're going to see it

pop up later in the video as well but

essentially the name of the polymerase

is kind of based

on what your starting point is and what

you're going to so we're starting with

double-stranded dna and we're trying to

make

rna we're going from dna to rna so this

polymerase is dna dependent rna

polymerase

so that's kind of how the naming works

here and we'll get into that a bit later

but that's how we get to the mrna and

that's going to be our viral protein

like we mentioned

earlier the other objective we said of a

virus

in this case is to duplicate or

replicate

its genome so that that duplication

could be sent off

for encapsidation and infection of new

hosts

because the virus just wants to infect

and spread and work fast right

so that's what it's doing that's what

it's coming to do make an mrna

to become viral protein and then uh

[Music]

replicate its genome for encapsulation

so if we look at figure b

here polyomaviridae this

genome is very small so as you can see

it doesn't really have it has limited

coding capacity here

it can't encode its own polymerase which

is why it's going to rely on the host

another thing i want you to keep in mind

is these are dna genomes that we're

looking at right now

so that's another reason why they can

rely on the host

because host machinery is already built

to work with dna

when we look at rna genomes a bit later

you'll notice that they do

a whole different thing they use their

own polymerases because

they can't rely on the host because rna

is very foreign to the host

so this is group two this is

single-stranded

dna genome uh so for this example

we are going to once again look at

figure a and

we start off with a single strand um and

we need dna synthesis to get to our

double-stranded dna

before we can produce an mrna right so

once again we're exploiting the hosts

dna polymerase

dna-dependent rna polymerase to get to

the mrna

production which is going to be go off

and

become the viral protein in the after

future steps

and then this double-stranded dna is the

template

for the duplication of the genome to get

back to our single

strand and that's going to be sent off

for encapsidation

so group 2 is relatively simple here

moving on to our final group

for the dna viral genomes this is group

seven

gapped double stranded dna so when we're

starting with

gapped double-stranded dna this gap must

first be filled so that we can generate

a completed

double-stranded dna molecule from which

we can generate an mrna strand

so that's the first step here we're

trying to get this gap filled and that

is done

in the nucleus so

now we have a fully formed

double-stranded dna and from there we

can generate our mrna which we've seen

before and that's going to be the path

going rightwards

so the boxed strand that's our mrna

which is going to go on to be the viral

protein and

you know keep going on from there so

then

going leftwards this is where we're

duplicating our genome so

from um double-stranded dna

um it makes an mr an rna that's

basically like the mrna

because it's plus single stranded rna

and this is going to encode a reverse

transcriptase

which is going to take this rna as a

template and make

the dna strand so it is reverse

transcriptase that's going to get us

back to the gapped double stranded

dna molecule from the rna

so if you recall a little bit earlier in

the video i mentioned

that we keep up with names of the

polymerases based on what your starting

point is and what the end point is

so we said dna dependent rna polymerase

was us going from dna to rna

so here actually when we're duplicating

our genome we're going from rna to dna

and we're using reverse transcriptase

but another name

for the reverse transcriptase is the

rna-dependent

dna polymerase so hopefully that makes

sense

okay so now that we've done the dna

genomes we're going to move on to the

rna genomes

so just a quick refresher we said that

dna genome viral dna genomes

exploit the host polymerase in order to

you know duplicate their genome and to

produce an

mrna from a dna template

rna viral genomes cannot necessarily

do this and this is because cells have

no rna-dependent rna polymerase

so to replicate their genome or

to make an mrna from an rna template

because the host doesn't have anything

that goes from rna to rna

whereas in dna genomes we the host

is you know built to work with dna so it

could obviously make

an mrna from a dna template so in this

case with rna since it can't do that it

needs to

encode its own polymerase all rna

viruses have to encode their own

polymerases

which also means that they need space in

their genomes in order to do this

so they do all of this through two

strategies

the first one is the rna dependent rna

polymerase

also known as the rdrp so this is

virally encoded

and i want you to recall that little

rule

i i mentioned earlier where i said

basically the naming of the polymerase

is it's easier to keep track

of the name and where it comes into play

based on what our template is and what

we're trying to go to

so if we're going from rna to make an

rna

we're using the rdrp if we were going

from

dna like in the dna genomes to make an

mrna

we're using a dna dependent rna

polymerase okay so now let's look at the

second

strategy the retro reverse transcriptase

known as the rt so we just looked at

reverse transcriptase

um in action with the gapped

double-stranded dna

and if you notice it was used when we

were going from an

rna to dna so

you can kind of guess what another name

for reverse transcriptase is

and that is rna-dependent dna polymerase

because it goes from rna to dna like in

the case of the gapped double-stranded

dna okay so

let's move on to our first rna

viral genome group and this is group

three this is the

double stranded rna viral genome

so we're only really going to pay

attention to the left side

figure a that's all we really need to

focus on here so

we start off with a double stranded rna

genome

and what happened is what happens here

is that we get

a transcription of one of the rna

strands

of the double-stranded rna genome to

single-stranded plus

rna which is our mrna right

the boxed green rna strand that is

always going to be our mrna if you've

noticed throughout this video

and that is going to go on to make our

viral protein or our virion

so in addition to this this

single stranded plus rna can also act as

a template

to make the negative rna strand

so for that strand synthesis that's

going to basically convert us back

to our double-stranded rna genome so

we've duplicated our genome now

and that is for that's going to go up

for packaging so one thing i want you to

know

is when we're using this plus single

stranded

rna as our um

template for the negative strand that

negative strand intermediate

is called our anti-genome

okay moving on to group four

this is the positive single stranded rna

genome so with this one

the positive rna genome is because it's

already single stranded it's basically

an mrna so it can be

translated directly into proteins by the

hosts

ribosomes so the genome of a positive

single-stranded rna virus

is actually very infectious when um

introduced into the host

so i want you to look at figure b there

there's an example and it says corona

viridae

that might sound a bit familiar to those

watching this through the pandemic

but so this is technically very

infectious because

it can be translated directly into

proteins

so as you can see our starting group

our starting product there it's already

boxed that genome because it's basically

mrna

that can go off and be our viral protein

immediately

um so also what happens here when we

want to duplicate

is that the negative rna strand is

generated

by the virally encoded rdrp

and then copied back into the plus

strand so that can go off for

encapsidation

moving on to group five this is the

negative single-stranded rna genome

so this is um negative

so what happens is that it must first be

copied to make

the positive strand so that we can get

our mrna

so that is the boxed one that's mrna

which is once again going to go off

to that's going to be our virion or the

viral protein

and the other objective we said of the

virus is to

duplicate the genome so

uh basically this um genome

is making it's the template to make our

positive strand which we've done

and that can be in turn copied to make

our negative strand

so we've duplicated it and that is sent

off for encapsidation

so in this case we have the rdrp working

because we're going from rna

template to an mrna when we were

starting off so the rdrp is working here

because we're going from rna to

rna we're not switching back and forth

between rna and dna

okay moving on to our last

rna genome type this is group six

this is the plus single-stranded rna

with a double-stranded

dna intermediate so

basically um what we're dealing with

here is we're starting with rna

and we're going to dna so the polymerase

that we're using

is going to be reverse transcriptase

it's the rna-dependent dna polymerase

because we're going from rna

going back to dna so reverse

transcriptase does that

so basically um the rna genome

our single strand is converted to double

stranded dna

so it's converted into this

double-stranded dna intermediate through

the retro

the reverse transcriptase and this

uh double-stranded dna is going to

become

integrated into the host genome

and this is going to serve as the

template to then produce the mrna which

we've seen before we know that

double-stranded dna we can get an mrna

from that

so that's going to go off to be our

viral protein and then

we can produce an a single stranded rna

which is

basically the same thing as mrna they're

the same thing

and this is to duplicate the original

genome because we want to always get

back to what the original was

so we duplicate that and that's going to

be for sent off for encapsidation

okay so that is the end of this video

um we've gone through groups one through

seven of the baltimore scheme

and their details and the different

types of

is used so hopefully that covers

all that you need for this topic in your

viral

vibrology classes so be sure to

subscribe to this channel and like this

video

and comment if you have any questions

concerning this material

also feel free to comment with any other

topics you would like brain boost to

make a video on and

we will have that up for you