A. Bruce

Cahoon

Courses Taught

• BIO1010, Principles of Biology
• BIO1011, Principles of Biology Laboratory
• BIO 3130, Plant Physiology and Cell Function
• BIO3600, Molecular Genetics

Research Interests & Recent Publications

My research focuses on two broad areas – Appalachian algal & microbial biodiversity and cell organelle gene expression.

Appalachian Algal & Microbial Biodiversity:

Our region of Appalachia is considered a biodiversity hotspot both colloquially and by professional biologists.  Interestingly, a review of the primary scientific literature provides very few published studies on this phenomenon, which begs the question, How do we know this?  The best known example of this diversity is the numerous endemic freshwater mussels found in the Clinch River system but little is documented about other groups of organisms, especially microscopic primary producers such as beneficial algae and bacteria.  To address the paucity of published accounts, UVA Wise students and I have been primarily surveying microscopic freshwater dwelling prokaryotes (bacteria) and eukaryotes (collectively known as “protists”) using genomics techniques such as organellar genome sequencing and meta-barcoding.  Genome sequencing allows us to archive the DNA sequences of whole organellar chromosomes from local organisms while meta-barcoding gives us the ability to identify many (up to thousands) of microbes from a single sample by using modern DNA sequencing methods. The “barcode” refers to a small section of genomic DNA found in all living things (often a ribosomal RNA gene) whose sequence allows one to positively identify a microbe by its DNA sequence. To date we have produced millions of DNA sequences and identified thousands of microbes from the Appalachian region of far Southwest Virginia.

Recent Publications related to Appalachian Algal & Microbial Biodiversity
* UVA Wise Student

A Bruce Cahoon, Katherine M. Johnson, Sydney M. Brown, Kalina M. Manoylov, James A. Nienow.  (2024) The chloroplast and mitochondrial genomes of two Gomphonema parvulum (Bacillariophyta) environmental isolates from South Carolina (USA) and Virginia (USA). Journal of Phycology

Kendall Davids*, Margie Tucker, Walter Smith, Bruce Cahoon (2023). The mitochondrial genome of Aneides aeneus (Green Salamander). eBio Notes 1:1-21

Lucie O Hornberger*, Isabella J. Maggard*, Robin A. Matthews & A. Bruce Cahoon. (2023) Cryptomonas pyrenoidifera organellar genomes and estimation of its ITS2 sequence diversity using lineage directed barcode primers.  Phycologia

A. Bruce Cahoon and Robert VanGundy (2022). Alveolates (Dinoflagellates, Ciliates, and Apicomplexans) and Rhizarians are the most common microbial eukaryotes in temperate Appalachian karst caves. Environmental Microbiology Reports.

Marvin W. Fawley, Karen P. Fawley, A. Bruce Cahoon (2021) Finding needles in a haystack – extensive diversity in the Eustigmatophyceae revealed by community metabarcode analysis targeting the RbcL gene using lineage-directed primers. Journal of Phycology

Kendall V. Morse*, Dylan R. Richardson*, Teresa L. Brown, Robert D. VanGundy, A. Bruce Cahoon (2021) Longitudinal metabarcode analysis of karst bacterioplankton microbiomes provide evidence of epikarst to cave transport and community succession. PeerJ: e10757

Blia Lor, Merry Zohn, Marcus J. Meade*, A. Bruce Cahoon and Kalina M. Manoylov (2021) A morphological and molecular analysis of a bloom of the filamentous green alga Pithophora. Water. 13:760

Brandon Thompson*, Dylan Richardson*, Robert D. Vangundy, A. Bruce Cahoon (2019) Metabarcoding comparison of prokaryotic microbiomes from Appalachian karst caves to surface soils in Southwest Virginia, USA.  Journal of Cave and Karst Studies 81:244-253

Grayson C. R. Proulex*, Blia Lor, Kalina M. Manoylov, A. Bruce Cahoon (2019) The chloroplast and mitochondrial genomes of the green alga Pediastrum duplex isolated from Central Georgia (USA). Mitochondrial DNA Part B 4:2

Katy Mullins*, Robert D. VanGundy, A. Bruce Cahoon (2019) Unexpected amounts of human DNA discovered in Appalachian karst cave systems. Lux: Undergraduate Scholarship at the University of Virginia’s College at Wise. 2:74-94

Roseanna M. Crowell*, James A. Nienow, and Aubrey Bruce Cahoon (2019)  The complete chloroplast and mitochondrial genomes of the diatom Nitzschia palea (Bacillariophyceae) demonstrate high sequence similarity to the endosymbiont organelles of the dinotom Durinskia baltica.  Journal of Phycology. 55:352-264

A. Bruce Cahoon, Ashley G. Huffman*, Megan M. Krager, Roseanna M. Crowell* (2018) A meta-barcoding census of freshwater planktonic protists in Appalachia – Natural Tunnel State Park, Virginia, USA. Metabarcoding and Metagenomics 2:e26939

Organelle RNA Processing:

Organelles (mitochondria and chloroplasts) are semi-autonomous entities within the cytoplasm of eukaryotic cells.  They were once free-living α-protoeobacteria (mitochondria) and cyanobacteria (chloroplasts) that were incorporated into pre-eukaryotic cells by a process known as endosymbiosis.  As a result, these organelles have their own genomes that are mostly circular chromosomes but in some cases are linear or composed of numerous fragments.  The genes remaining on these organelles tend to be conserved and carry the rRNAs and tRNAs necessary for completing gene expression.  Mitochondrial genomes (chondriomes) tend to have components of the electron transport chain and chloroplasts tend to have maintained components necessary for photosynthesis.  For both organelles, thousands of other proteins necessary for their maintenance and function are encoded by genes found in the nucleus and must be imported from the cytosol into the organelles.  These organelles are completely dependent upon and inseparable from the host eukaryotic cells, and have evolved unique gene expression processes with elements of both prokaryotic or eukaryotic nuclear systems.

The first stage of gene expression is the process of transcription where a RNA copy is made from DNA template.  In organelles, many coding regions (genes) may occur on a single polycistronic RNA called a primary RNA.  Several modifications must occur before mRNAs can be translated into protein, these steps are collectively known as RNA processing. First, each of the individual genes must be excised from the primary transcripts by endonuclease enzymes. Next, in some organisms (most notably land plants), the sequence of the RNA may be changed by a process called RNA editing.  RNA editing enzymes are best known for changing cytosines to uracils and modifying RNAs transcribed from genes with DNA mutations that would make the gene inexpressible.  Next, polynucleotide tails, such as polyA and polyC, may be added to the 3’ ends of the mRNAs as a final step prior to translation.  There is also evidence that the addition of a 3’ poly-adenine tail marks mRNAs for degradation by exonucleases.

My students and I use molecular genetic tools to explore how the hybrid gene expression systems in endosymbiotic organelles (mitochondria and chloroplasts) work and how they differ from more commonly studied bacterial and eukaryotic systems.  Recent discoveries made by UVA Wise students include mRNA circularization in human and algal mitochondria and the presence of polyU additions on the mRNAs of green algal chloroplasts.

Selected Publications Related to Organelle RNA Processing
* UVA Wise Student

Grayson C.R. Proulex*, Marcus J. Meade*, Kalina M. Manoylov, A. Bruce Cahoon (2021). Mitochondrial mRNA processing in the chlorophyte alga Pediastrum duplex and streptophyte alga Chara vulgaris reveal an evolutionary branch in mitochondrial mRNA processing. Plants, 10:576

Marcus Jerryd Meade*, Grayson C. R. Proulex*, Kalina M. Manoylov, A. Bruce Cahoon. (2020) Chloroplast mRNAs are 3’ polyuridylylated in the green alga Pithophora roettleri (Cladophorales). Journal of Phycology.

Landon G. Mance*, Ishaat Mawla*, Steven M. Shell, A. Bruce Cahoon (2020) Mitochondrial mRNA fragments are circularized in a human HEK cell line. Mitochondrion. 51:1-6

A. Bruce Cahoon and Ali A. Qureshi(2018)Leaderless mRNAs are Circularized in Chlamydomonas reinhardtii Mitochondria. Current Genetics. 64:1321-1333

Christen M. Klinger, Lucas Paoli, Robert Newby, Matthew Yu-Wei Wang, Hyrum D. Carroll, Jeffrey D. Leblond, Christopher J. Howe, Joel B. Dacks, Bruce Cahoon, Richard G. Dorrell, and Elisabeth Richardson  (2018) Plastid transcript editing across dinoflagellate lineages shows lineage-specific application but conserved trends.  Genome Biology and Evolution. 10:1019-1038

Cahoon, A. B., Nauss, J.N.*, Stanley, C.D.*, Qureshi, A. (2017) Deep Transcriptome Sequencing of Two Green Algae, Chara vulgaris and Chlamydomonas reinhardtii, Provides no Evidence of Organellar RNA Editing.  Genes 8(2)