Lines of study

Prelude

Light is an important and ubiquitous environmental signal, and an essential energy source. It corresponds to electromagnetic radiation extending from high energy gamma and X-rays to low energy radio waves, with that in the 380–760 nm wavelength range, detectable by the human eye, being described as visible light.

The ability to sense and respond to light is vital for most living organisms. It enables human vision. Plants, algae and photosynthetic bacteria convert sunlight into chemical energy, which accounts for most of the fixed biomass and molecular oxygen. Light also directly or indirectly signals diverse biological processes, including DNA repair, circadian rhythms, taxis, development, morphology, physiology, and virulence, and also biosynthetic reactions. However, light can also cause cell damage and death. This is because light interacts with photosensitive biomolecules like porphyrins, chlorophyll, or flavins to generate highly reactive oxygen species (ROS) that attack cellular DNA, proteins and lipids. Various cellular strategies have therefore also evolved to avoid, minimize, or repair light-induced damage.

Among living organisms, bacteria have developed many remarkable ways to sense, respond to, and utilize light. Responses to light leading to photosynthesis, protection against photooxidative damage, and other processes have been extensively studied in many bacterial species, from which fascinating details about the cellular machinery and  molecular mechanisms involved have emerged continually. We study how the bacterium Myxococcus xanthus senses and responds to light.

About Myxococcus xanthus

Classification: Bacteria; Proteobacteria; Deltaproteobacteria; Myxococcales; Cystobacterineae; Myxococcaceae; Myxococcus

M. xanthus is a non-pathogenic, Gram-negative, soil bacterium found in damp soil rich in organic matter. It is rod-shaped (typically 5 mm long, 0.5 mm wide) and ~10 times larger in size than Escherichia coli, the most studied and understood bacterial model organism. The circular M. xanthus genome is large (~9.14 Mbp), GC-rich (69%) and encodes about 7200 proteins and 80 structural RNAs. In comparison, the intensely studied model eukaryotic unicellular organism, the baker's yeast or Saccharomyces cerevisiae, has 16 linear chromosomes, a total length of ~12 Mbp, ~38 % GC content, and encodes about 5800 proteins.

M. xanthus is a chemoorganotroph that obtains its energy by oxidizing organic compounds. It is a predatory bacterium whose prey are other bacteria and unicellular microorganisms. Groups of cooperating M. xanthus cells hunts like a “wolf pack” by swarming through the soil and feeding by secreting toxins and digestive enzymes to immobilize and degrade prey. Pili found only at the cell poles enable gliding motility. Two motility patterns are employed each with separate gene systems : adventurous (A-motility) involving isolated cells, and social (S-motility) involving groups of cells. M. xanthus swarm and predate when food is available. When starved the group of M. xanthus cells undergo a complex development program with sophisticated intercellular signaling to form a multicellular fruiting body that contains spores from which motile cells can reappear when nutrients are available.

M. xanthus has therefore served as a bacterial model to investigate motility, predation, cell-cell interactions and kin recognition, multicellular development. It provides a powerful system to the evolution of social behaviour among microbes in an ecological context. A source of several useful secondary metabolites, their synthesis and production is also an area of active ongoing research. We use it to study light sensing and response.

The Myxococcus xanthus light response

 

(See our recent up to date (as of 2021) review for details on about the M. xanthus light response:

• Padmanabhan S, et al. “Light-triggered carotenogenesis in Myxococcus xanthus: New paradigms in photosensory signaling, transduction and gene regulation” Microorganisms 9: 1067. DOI:  10.3390/microorganisms9051067 )
  

Wild-type strains are yellow in the dark due to noncarotenoid, light-sensitive pigments identified in 2005 named DKxanthenes, but turn red when exposed to blue light because of the synthesis of carotenoids.

 

 

Carotenoids 

 

Carotenoids are richly colored pigments (light yellow to deep red) that protect cells against photooxidative damage by quenching highly reactive oxygen species (ROS) like singlet oxygen (¹O₂), superoxides, peroxides and hydroxyl radicals produced upon illumination that can destroy cellular components like DNA, protein and lipids.

Carotenoid biosynthesis de novo occurs in all photosynthetic organisms (plants, algae or bacteria) and in many non-photosynthetic fungi, archaea and bacteria, whereas animals, save some strikingly few exceptions, do not synthesize carotenoids but obtain them exogenously. 

 

Light and carotenoid biosynthesis in M. xanthus

Light and oxygen-related species like ¹O₂ are among the principal environmental factors involved in signaling and triggering carotenoid biosynthesis.

In M. xanthus, light/¹O₂ induce a regulated transcriptional response employing novel light sensing, signal transduction and gene regulation mechanisms that leads carotenogenesis. The structural genes encoding enzymes for carotenoid synthesis, which are switched off in the dark and turned on in the light, are found at two genomic loci.

The carB locus encodes nine structural genes for carotenoid synthesis and two for transcription regulators, CarA and CarH. These are expressed from a primary s^A-dependent promoter, P_B.

The remaining isolated structural crtIb gene is expressed from a promoter, P_I, dependent on an ECF-s factor CarQ.

(Numbers the correspond to the genome locus tag (MXAN_xxxx) of each of these genes).

Carotenoid biosynthesis in M. xanthus occurs via the largely conserved pathway that derives from the mevalonate (MVA) pathway for isoprenoid synthesis:

Two light-sensing mechanisms to trigger carotenoid biosynthesis in M. xanthus

 1. Direct sensing of UV, blue or green light and gene regulation by CarH, the defining member of a large B₁₂-based photoreceptor family that uses coenzyme B₁₂ or 5´-deoxyadenosylcobalamin (AdoCbl), a biological form of vitamin B₁₂, as the light-sensing chromophore.

Coenzyme B₁₂ or 5´-deoxyadenosylcobalamin (AdoCbl)

 

CarH mode of action:

• In the dark, AdoCbl-bound CarH binds to its operator at P_B to block access to RNAP-s^A and repress transcription.
• Light (UV, blue or green) inactivates CarH to prevent its binding to operator, allowing P_B access to RNAP-s^A and transcription initiation.

Light-dependent regulation of transcription by CarH relies on modulation of its oligomeric state by AdoCbl and light.

 

 Structures of the Thermus thermophilus CarH AdoCbl-bound tetramer, free and DNA-bound forms, and the light-exposed monomer determined.

Protomer: N-terminal MerR-type DNA-binding domain (blue) + C-terminal AdoCbl binding domain with AdoCbl (sticks, magenta) sandwiched between a four-helix bundle subdomain (golden) and a Rossmann fold subdomain (green).

 

 

 Under construction!