SbtB protein


SbtB, which stands for sodium-bicarbonate-transporter B, is a protein found in bacteria. This small soluble protein has been classified as a new member of the P-II family that is involved in signal transduction. This protein has been demonstrated to participate in numerous processes including carbon sensing mechanisms in cyanobacteria.

Carbon concentrating mechanisms

Currently, most of the oxygen on planet earth derives from oxygenic photosynthesis. Some phototrophic prokaryotes such as cyanobacteria developed the ability to carry out oxygenic photosynthesis around 2.7 billion years ago. Moreover, 2 billion years ago planet earth was struck with "The Great Oxygenation event" also known as the oxygen crisis. Rising levels of atmospheric, mainly due to oxygenic photosynthesis carried out by cyanobacteria nearly caused the mass death of anaerobic organisms. Having to face the evolutionary pressure of dropping ambient levels, cyanobacteria coped by evolving carbon concentrating mechanisms. Thus, these carbon concentrating mechanisms, also known as "DIC-pumps", are found in most photosynthetic microorganisms, such as unicellular green algea and cyanobacteria. These environmental adaptations vastly improve photosynthetic performance and survival. Indeed, this is achieved by accumulating intracellular inorganic carbon providing elevated levels around the primary fixing enzyme, Rubisco.
Although, until very recently it was poorly understood how these photoprotic procaryotes could sense the fluctuations in inorganic carbon, scientists have recently discovered that a gene, SbtB, encoding a small soluble protein which may have an important role in the process. SbtB participates in sensing fluctuations of concentrations in the environment and therefore adjusts fixation in according to its surroundings.
This discovery has been groundbreaking as earth and all of its inhabitants depend on photosynthetic carbon dioxide fixation to form organic carbon. In addition, cyanobacteria are some of the oldest organisms on earth and any additional knowledge about how they operate internally offers insight on the earliest forms of life on earth. These procaryotic organisms may enclose the answers to some of the most challenging questions ever posed in regards to the origin of life as we know it.

Structure

'SbtB' is a homo trimeric protein. The monomer consists of 120 amino acid residues with molecular weight of 11875 Da. In addition, the monomer contains the following secondary structures:
A crystallographic structure of SbtB protein has been obtained from ScSbtB The apo-ScSbtB shows a canonical ferredoxin-like fold in every subunit. As seen before, the molecular structure of the three subunits is identical. At the N terminus the first beta-sheets face the C terminus. The carboxyl terminus of the last cysteine forms a hydrogen bond with the N terminus. This interaction allows the stabilization of N and C terminus.

Ligand binding

ScSbtB has shown to bind ATP, ADP and cAMP with dissociation constants of 46, 19, and 11 μM respectively. The ring opened form of cAMP, AMP binds with much lower affinity.

Gene

This protein is coded by the 'SbtB' gene, also called 'CMM_2535' gene. Assembled in the genome of the clavibacter michiganensis specie, It is a putative serine protease gene that belongs to the PTHR10795 family, which contains 23545 species.
It is assembled in the genome of the species Clavibacter michiganensis. This species is part of the family Microbacteriaceae, and has five subspecies. The subspecies that contains this gene in its genome is C. m. subsp. michiganensis. The latter is involved in bacterial wilt and canker of tomato.
It's located in the circular chromosome of this kind of microorganisms, which contains 2984 coding genes and 3,297,891 bit/s. Specifically, sbtB is located between the 2,851,656-2,855,336 bit/s and is composed by six different motifs which are shown below.

Gene motifs

In terms of the aminoacid sequence, the sbtB gene has the following motifs:
MotifFromToE value
Peptidase Inhibitor I9851841.4e-11
Peptidase S8 2136946.3e-42
PA domain4855591.5e-09
FN 3 67358285.9e-23
Bacterial pre-peptidase C-terminal domain8959610.002
Bacterial Ig-like domain 114612241.6e-11

Chromosome statistics

The circular chromosome of this bacteria specie has the following characteristics:
Length 3,297,891
Coding genes2,984
Non coding genes106
Pseudogenes24

Transcript gene: sbtB-1

It has a transcript gene called 'sbtB-1'. This specific transcript gene has 1 coding exon and is annotated with 23 domains. In term of statistics, it has a transcript length of 3681 bit/s and a translation length of 1226 residues. It is located between the 2,855,336 - 2,851,656 base pairs.

Function

Serine-type endopeptidase activity

SbtB is part of the S8A family inside the SB Clan as classified by the peptidise database MEROPS as well as uniprot. This family is characterised by their main function: the hydrolysis of peptide bonds. This is possible due to the catalytic triad in their active site of their protein sequence: Aspartate, Serine and Histidine. The serine nucleophile responsible for the cleave of peptide bonds is activated by the contribution of the acidic residue and the basic residue.

Carbon concentration

SbtB is part of the cyanobacterial CCM system. It acts as a post-translational regulator of the SbtA protein by binding to it during the dark hours to prevent rising levels of Na+ from growing and becoming toxic for the cyanobacterial cell. The SbtB protein is crucial for the photosynthetic process as it inhibits the SbtbA protein via direct interaction between both proteins. It is therefore a regulator of the Na+/HCO3− transporter and is responsible for the cyanobacterial inorganic carbon response via cAMP sensing.

Importance in binding processes

SbtB not only takes part in the binding process of ATP and ADP, but is also the first ever known protein to bind the nucleotide cAMP. This cyclic nucleotide is a single-phosphate nucleotide with a cyclic bond between the phosphate and the sugar, and is a derivative from ATP. Furthermore, cAMP is a key-signaling molecule in a wide range of processes including the state of carbon metabolism in all organisms. Until now cAMP was widely known for its important role in the maintenance of glucose balance, but in identifying SbtB researchers have discovered a new carbon sensing mechanism through cAMP. SbtB's role is gaining importance as research shows it is a direct participer in the sensing of inorganic carbon fluctuation in cyanobacteria.