SbtB, which stands for sodium-bicarbonate-transporter B, is a

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respon ...

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 Signal transduction is the process by which a chemical or physical signal is transmitted through a cell as a series of molecular events, most commonly protein phosphorylation catalyzed by protein kinases, which ultimately results in a cellular ...

. This protein has been demonstrated to participate in numerous processes including carbon sensing mechanisms in cyanobacteria.

Carbon concentrating mechanisms

Most of the oxygen on planet earth derives from

oxygenic photosynthesis Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that, through cellular respiration, can later be released to fuel the organism's activities. Some of this chemical energy is stored in ...

. 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 (CCM). Thus, these carbon concentrating mechanisms, also known as "DIC-pumps", are found in most photosynthetic microorganisms, such as unicellular green algae and cyanobacteria. These environmental adaptations vastly improve photosynthetic performance and survival. Indeed, this is achieved by accumulating intracellular inorganic carbon (Ci) providing elevated levels around the primary fixing enzyme, Rubisco. Although previously, it was poorly understood how these photoprotic procaryotes could sense the fluctuations in inorganic carbon (Ci), scientists have discovered that a gene, SbtB, encoding a small soluble protein (SbtB) may have an important role in the process. SbtB participates in sensing fluctuations of concentrations in the environment and therefore adjusts fixation according to its surroundings. This discovery is important 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 reveal information regarding challenging questions posed in regards to the

origin of life In biology, abiogenesis (from a- 'not' + Greek bios 'life' + genesis 'origin') or the origin of life is the natural process by which life has arisen from non-living matter, such as simple organic compounds. The prevailing scientific hypothes ...

Structure

'SbtB' is a homo trimeric protein. The monomer consists of 120

amino acid residues Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers specifically polypeptides formed from sequences of amino acids, the monomers of the polymer. A single amino acid monomer may ...

with

molecular weight A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and bioch ...

of 11875 Da.; * In addition, the monomer contains the following

secondary structure Protein secondary structure is the three dimensional form of ''local segments'' of proteins. The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary struct ...

s: * Beta-sheets (34% of the chain): there is a total of 4 strands composed by a total of 41 residues. * Helical structures (26% of the chain): 4 helical structures. The first one consisting of a 3/10-helix and an alpha helix. The rest are exclusively made up by alpha helix structures. * 3 T-turns. The flexible T loop is mostly disordered which is common in the P_II like proteins * the beta sheets and alpha-helical structures are connected by loops. A crystallographic structure of SbtB protein has been obtained from ScSbtB ( Synechocystis sp.) 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 N-terminus (also known as the amino-terminus, NH2-terminus, N-terminal end or amine-terminus) is the start of a protein or polypeptide, referring to the free amine group (-NH2) located at the end of a polypeptide. Within a peptide, the amin ...

the first beta-sheets face the

C terminus The C-terminus (also known as the carboxyl-terminus, carboxy-terminus, C-terminal tail, C-terminal end, or COOH-terminus) is the end of an amino acid chain (protein or polypeptide), terminated by a free carboxyl group (-COOH). When the protein is ...

. 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 ATP may refer to: Companies and organizations * Association of Tennis Professionals, men's professional tennis governing body * American Technical Publishers, employee-owned publishing company * ', a Danish pension * Armenia Tree Project, non ...

ADP Adp or ADP may refer to: Aviation * Aéroports de Paris, airport authority for the Parisian region in France * Aeropuertos del Perú, airport operator for airports in northern Peru * SLAF Anuradhapura, an airport in Sri Lanka * Ampara Air ...

and cAMP with

dissociation constant In chemistry, biochemistry, and pharmacology, a dissociation constant (K_D) is a specific type of equilibrium constant that measures the propensity of a larger object to separate (dissociate) reversibly into smaller components, as when a complex ...

s (K_d) 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 In biology, the word gene (from , ; "... Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a b ...

, also called 'CMM_2535' gene. Assembled in the

genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ...

of the

clavibacter michiganensis ''Clavibacter michiganensis'' is an aerobic non-sporulating Gram-positive plant pathogenic actinomycete of the genus '' Clavibacter''. ''Clavibacter michiganensis'' has several subspecies. ''Clavibacter michiganensis'' subsp. ''michiganensis'' ...

specie, It is a putative serine protease gene that belongs to the PTHR10795 family, which contains 23545 species. It is assembled in the

of the species ''

Clavibacter michiganensis ''Clavibacter michiganensis'' is an aerobic non-sporulating Gram-positive plant pathogenic actinomycete of the genus '' Clavibacter''. ''Clavibacter michiganensis'' has several subspecies. ''Clavibacter michiganensis'' subsp. ''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 A chromosome is a long DNA molecule with part or all of the genetic material of an organism. In most chromosomes the very long thin DNA fibers are coated with packaging proteins; in eukaryotic cells the most important of these proteins ar ...

of this kind of microorganisms, which contains 2984 coding genes and 3,297,891 bps (base pairs). Specifically, sbtB is located between the 2,851,656-2,855,336 bps and is composed by six different motifs which are shown below.

Gene motifs

In terms of the aminoacid sequence (1224 aminoacids), the sbtB gene has the following motifs:

Chromosome statistics

The circular chromosome of this bacteria specie has the following characteristics:

Transcript gene: sbtB-1

It has a transcript gene called 'sbtB-1'. This specific transcript gene has 1 coding

exon An exon is any part of a gene that will form a part of the final mature RNA produced by that gene after introns have been removed by RNA splicing. The term ''exon'' refers to both the DNA sequence within a gene and to the corresponding sequenc ...

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 bond In organic chemistry, a peptide bond is an amide type of covalent chemical bond linking two consecutive alpha-amino acids from C1 (carbon number one) of one alpha-amino acid and N2 ( nitrogen number two) of another, along a peptide or protein c ...

s. This is possible due to the

catalytic triad A catalytic triad is a set of three coordinated amino acids that can be found in the active site of some enzymes. Catalytic triads are most commonly found in hydrolase and transferase enzymes (e.g. proteases, amidases, esterases, acylases, l ...

in their active site of their protein sequence:

Aspartate Aspartic acid (symbol Asp or D; the ionic form is known as aspartate), is an α-amino acid that is used in the biosynthesis of proteins. Like all other amino acids, it contains an amino group and a carboxylic acid. Its α-amino group is in the pro ...

Serine Serine (symbol Ser or S) is an α-amino acid that is used in the biosynthesis of proteins. It contains an α- amino group (which is in the protonated − form under biological conditions), a carboxyl group (which is in the deprotonated − for ...

and

Histidine Histidine (symbol His or H) is an essential amino acid that is used in the biosynthesis of proteins. It contains an α-amino group (which is in the protonated –NH3+ form under biological conditions), a carboxylic acid group (which is in the ...

(the triad is presented in this specific order in the S8 family). The serine nucleophile responsible for the cleave of peptide bonds is activated by the contribution of the acidic residue (Asp) and the basic residue (His).

Carbon concentration

SbtB is part of the cyanobacterial CCM (CO₂-concentrating mechanism) system. It acts as a post-translational regulator (inhibitor) of the SbtA protein (one of the three sodium-dependant bicarbonate (Na⁺/HCO3⁻) symporters in the cytoplasmic membrane) 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

and

, but is also the first ever known protein to bind the nucleotide cAMP (Cyclic adenosine monophosphate). This

cyclic nucleotide A cyclic nucleotide (cNMP) is a single-phosphate nucleotide with a cyclic bond arrangement between the sugar and phosphate groups. Like other nucleotides, cyclic nucleotides are composed of three functional groups: a sugar, a nitrogenous base, ...

is a single-phosphate

nucleotide Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecul ...

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.

References

{{reflist Proteins