Structure and function of sigma factors

Question 1

What determines the number of different sigma factors that an organism has?

Answer 1

The stability of their environment

Question 2

Would a bacterial species that is an intracellular parasite have a lot of different sigma factors or just a few? Why?

Answer 2

Only one that transcribes everything. Their environment is so stable because they can’t exist outside a host cell

Question 3

Would a bacterial species that is a gut commensal species have a lot of different sigma factors or just a few? Why?

Answer 3

Have a handful, since their environment is still very stable. But not as stable as the inside of a eukaryotic cell

Question 4

Would a bacterial species that is lives in soil or water have a lot of different sigma factors or just a few? Why?

Answer 4

They would have a ton of different sigmas. Their environment fluctuates widely, and have to be able to deal with large changes in temperature, nutrient availability, and stress

Question 5

What are the two main families of sigma factors?

Answer 5

Sigma 70 and sigma 54

Question 6

How are sigma factors grouped into families?

Answer 6

Structural and functional similarities

Question 7

What sigma factors are included in the sigma 70 family? What consensus sequences do they bind to?

Answer 7

All primary and some alternative sigmas. They recognize and bind to -10 and -35 promoter motifs

Question 8

What sigma factors are included in the sigma 54 family? What consensus sequences do they bind to?

Answer 8

Some alternative sigmas. They bind to -12 and -24 consensus sequences, and can’t initiate transcription without help from an activator bound to an enhancer

Question 9

What proteins bind to enhancers that will then allow sigma 54 factors to initiate transcription?

Answer 9

Bacterial enhancer binding proteins (bEBPs) that use ATP

Question 10

What are the similarities between sigma 70 and sigma 54 factord?

Answer 10

None. There are no structural, sequence, or mechanism similarities

Question 11

What are the 4 functional domains in sigma 70? What do they do?

Answer 11

1. Region 1, prevents sigma from binding to DNA when it isn’t bound to the RNAP core
2. Region 2, recognizes and binds the -10 consensus sequence
3. Region 3, binds to RNAP core and to DNA
4. Region 4, recognizes and binds to the -35 consensus sequence

Question 12

Why does the first functional domain in sigma 70, preventing it from binding to DNA when it isn’t bound to the RNAP core, only typically found in primary sigmas?

Answer 12

They’re around and active all the time. The cell doesn’t want them binding to promoters and blocking transcription. Region 1 will be in a conformation that blocks sigma binding to DNA, but it changes conformation when it binds to an RNAP core

Question 13

What are 3 experimental methods to determine which regions of a promoter?

Answer 13

1. Structural analysis, look for DNA binding motifs
2. Sequence homology with already characterized sigmas
3. Mutational analysis

Question 14

What are the 4 structural groups within the sigma 70 family?

Answer 14

Group 1: primary sigmas
Group 2: alternative sigmas
Group 3: more alternative sigmas
Group 4: extracytoplasmic sigmas

Question 15

What type of sigma factors are included in Group 1 sigma 70 factors?

Answer 15

Primary/housekeeping sigmas. Always expressed and always active because they’re essential for cell growth and survival

Question 16

What type of sigma factors are included in Group 2 sigma 70 factors?

Answer 16

Alternative sigmas that are structurally similar to Group 1 sigmas. But they aren’t essential for growth

Question 17

What type of sigma factors are included in Group 3 sigma 70 factors?

Answer 17

Alternative sigmas that are less similar to Group 1 sigmas. Used to activate regulons in response to specific signals

Question 18

What type of sigma factors are included in Group 4 sigma 70 factors?

Answer 18

Extracytoplasmic alternative sigmas. Involved in responding to extracellular signals

Question 19

Why don’t promoters for housekeeping genes have to be “perfect,” and can diverge a bit from the ideal consensus sequences?

Answer 19

Primary sigmas are pretty flexible, and have strong DNA melting capabilities. They can still form the open complex from a variety of combos of promoter motifs

Question 20

Why do Group 3 and 4 sigmas require near perfect promoters to initiate transcription?

Answer 20

They don’t have as strong of DNA melting capabilities as primary sigmas, and require the -10, extended -10, and -35 consensus sequences with the right spacing

Question 21

Why wouldn’t the cell just want every promoter to be perfect and identical?

Answer 21

Having them different and imperfect allows for better regulation. It ensures that only certain sigmas transcribe certain genes, and the differences between them let sigmas recognize the right promoters

Question 22

What is a regulon?

Answer 22

A set of genes that are regulated together by transcription initiation with the same sigma factor. Includes every gene that has its transcription activated by the same sigma

Question 23

What common features would all genes in a regulon share?

Answer 23

Their promoters will all have relatively similar consensus sequences and spacing